<blockquote>I don't remember how it works atm, but if the Dehacked plugin can modify the map names and parts of the map metadata, we should retain that functionality (if possible).</blockquote>
I've recently done a bit of work on the Dehacked plugin. I recall - support for customising map metadata is implemented by patching the MapInfo defs held in Doomsday directly.

<blockquote>where values can be defined via Values in DED - could these internal defaults be removed from the Game libraries also?</blockquote> The Values def was added for that purpose exactly. All the hardcoded values like maximum healths and the amounts of ammo received from items should be defined (only) as Values. It is the easiest way to allow customization.